The use of digital 3D models in the dental market is becoming more prevalent. These models can be acquired in vivo using an intra-oral scanner or off-line by laser scanning of a traditional impression. The digital 3D models can be used for various clinical tasks including treatment planning, and crown and implant preparation. The models can also be used in diagnostic aides, for example to assess tooth wear and gingival recession. The digital 3D models are usually obtained in a random orientation and not fixed to a particular coordinate system. Accordingly, a need exists to align intra-oral digital 3D models to a given coordinate system for diagnostic or other purposes.